First, they estimate linkage evidence across the whole genome using the pooled sample and empiric P-values generated by simulations (i.e. generating empiric P-values based on 1000 replicates per chromosome using the exact marker information from the individual scans; for methods, see Ogdie et al.). Second, they performed an unweighted rank-based genome search meta-analysis (GSMA) of the two genome scans.

Basic Result

There is evidence for linkage within each individual study and significant evidence for a risk gene on 5p13 based on the pooled data. While the UCLA data contribute heavily to the joint linkage peak at 5p13, GSMA yields a pointwise significant PAR at that region, indicating a nominally significant overlap of rank-ordered bins that is independent of the varying signal strengths in the two samples. GSMA defined six bins with PAR <0.05 (~5p13, 11q25, 13q34,15q26, 16q23, and 20q13), which is in fact the exact expectation under the null distribution of two unrelated linkage scans, suggesting that there are few common effect loci between the two studies. In aggregate, both the pooled linkage analysis and the GSMA indicate that there is a lack of overlap of linkage peaks with the exception of chromosome 5p13.